BioC 2.14: CHECK report for cellGrowth on petty

Package: cellGrowth

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellGrowth_1.8.0.tar.gz

StartedAt: 2014-10-07 21:06:00 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:07:59 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 119.6 seconds

RetCode: 0

Status:  OK

CheckDir: cellGrowth.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellGrowth_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/cellGrowth.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellGrowth/DESCRIPTION’ ... OK
* this is package ‘cellGrowth’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cellGrowth’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘locfit’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘locfit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotPlate : strip.plate: no visible global function definition for
  ‘trellis.par.get’
plotPlate : strip.plate.left: no visible global function definition for
  ‘trellis.par.get’
wellDataFrame: no visible binding for global variable ‘use’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'plot.cellGrowthFit':
  ‘plot.cellGrowthFit’

S3 methods shown with full name in documentation object 'plot.well':
  ‘plot.well’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [76s/86s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
fitCellGrowths 55.073  3.593  68.133
wellDataFrame   5.594  0.078   5.693
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/cellGrowth.Rcheck/00check.log’
for details.

* installing *source* package ‘cellGrowth’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cellGrowth)

name	user	system	elapsed
bandwidthCV	4.330	0.040	4.607
baranyi	0.011	0.001	0.014
fitCellGrowth	0.156	0.005	0.179
fitCellGrowths	55.073	3.593	68.133
getRowColumn	0.002	0.000	0.002
getWellIdsTecan	1.193	0.037	1.236
gompertz	0.014	0.001	0.016
guessCellGrowthParams	0.054	0.003	0.060
logistic	0.012	0.002	0.014
plot.cellGrowthFit	1.203	0.036	1.246
plotPlate	2.105	0.027	2.136
readGenios	0.061	0.005	0.068
readYeastGrower	1.213	0.038	1.254
rosso	0.008	0.001	0.010
standardWellId	0.002	0.000	0.001
wellDataFrame	5.594	0.078	5.693